The intestinal tract is an important digestive organ and detoxification organ of the human body, and its circling structure is vividly called the “second brain” of the human body. There are hundreds of millions of bacterium in the intestinal tract. These bacteria live in mutual benefit with the body, provide energy and nutrients for the host and themselves through fermented food, participate in the metabolism of the body, and form a metabolic mode of cometabolism between the host and the symbiotic flora. In addition, intestinal flora can also help the body resist the invasion of pathogens, promote human health, and resist diseases. More and more studies have shown that when the body is subjected to exogenous or endogenous stimuli, the microbial flora in the intestinal will change, and the disturbance of intestinal flora is closely related to the occurrence and development of inflammatory bowel diseases, metabolic diseases, immune system diseases, mental system diseases, and tumors. This article reviews the research progress of the intestinal flora affecting the pathogenesis of various diseases, aiming to provide new references and ideas for the clinical treatment of diseases.